That's changing the layer of the trace, from top to bottom. Note the vias (circular elements in the design) where the color transition occurs.
To the OP: Looks great! I like the approach for modules, I've often wished Eagle had an easier way to achieve this =) A question though, it looks like there's only one ground source allowed? Or, can those properties be changed? I prefer to separate AGND from GND when I have both analog and digital interfaces to the outside world.
At this point there is indeed only one ground label, but if you use the generic label you can create as many as you like. Nets in the schematic that are connected to labels with the same name are merged when switching to PCB.
To the OP: Looks great! I like the approach for modules, I've often wished Eagle had an easier way to achieve this =) A question though, it looks like there's only one ground source allowed? Or, can those properties be changed? I prefer to separate AGND from GND when I have both analog and digital interfaces to the outside world.